Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011241.1 Kokia drynarioides strain JFW-HI SEQ_126219, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9099
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Found at i:2551 original size:17 final size:17
Alignment explanation
Indices: 2529--2576 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2519 ACCTTAATCC
2529 TAACCCTTAA-AAAACCT
1 TAACCC-TAATAAAACCT
*
2546 TAACCCTAATAAAACCC
1 TAACCCTAATAAAACCT
* *
2563 TAAACCTAACAAAA
1 TAACCCTAATAAAA
2577 TTATAAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (17 bp):
TAACCCTAATAAAACCT
Found at i:4400 original size:95 final size:94
Alignment explanation
Indices: 4223--4418 Score: 218
Period size: 95 Copynumber: 2.1 Consensus size: 94
4213 TCGATTAGCT
* * * * **
4223 TTGTTGAAAAACACAAATGGGATGAAATTTTGTGGCTTATGATTGGTGGATGGGATCCAAAAATA
1 TTGTAGAAAAACACAAATGGGATCAAATTTTGTGGCTTATGATTAGTGAATGAAATCCAAAAATA
* *
4288 TCTGATACAGTAAGCACTAAGCTGTTATA
66 TCTGATACAGTAAGCACTAAGCAGTAATA
* *
4317 TTGTAGAAAAACACAAATGGGATCAAATTTTTGTGGTTTTTGATTAGTGAATGAAA-CTCAAAAG
1 TTGTAGAAAAACACAAATGGGATCAAA-TTTTGTGGCTTATGATTAGTGAATGAAATC-CAAAA-
* *
4381 TATAT-TG-TGCAGTATGCACTAAGCAGTAATA
63 -ATATCTGATACAGTAAGCACTAAGCAGTAATA
4412 TATGTAG
1 T-TGTAG
4419 CCCTTAATCC
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
94 26 0.31
95 48 0.56
96 7 0.08
97 4 0.05
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (94 bp):
TTGTAGAAAAACACAAATGGGATCAAATTTTGTGGCTTATGATTAGTGAATGAAATCCAAAAATA
TCTGATACAGTAAGCACTAAGCAGTAATA
Found at i:7476 original size:209 final size:209
Alignment explanation
Indices: 7117--7992 Score: 1204
Period size: 209 Copynumber: 4.2 Consensus size: 209
7107 CAATTATCCA
* * * * * * *
7117 AAACAAGTGAGGCGATCATCTTCCTGATAAGATACTAAGAAGTATACCAACTCAATGAAATCATA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCA-A
* *
7182 -TTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCCCGATGAGATACTGAGAAGCAGGTCAAAGC
65 GCTCAAAGTGAGCAAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGC
* * * *
7246 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
129 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGAT
* **
7311 ACAGAGAAGTGGATCA
194 ACAGAGAAGCGGATTG
* *
7327 AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG
* *
7392 CTCAAAGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGTAGGTCAAAGCAA
66 CTCAAAGTGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAA
* * *
7457 TAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGTGAACCAAATTCACCTTCCTGATGAGATAT
131 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATAC
7522 AGAGAAGCGGATTG
196 AGAGAAGCGGATTG
*
7536 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCCAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG
* *
7601 CTCAAAGTGAGCAAAACTTCAAACCCCAGCTTCCTGATGAGAAACTGAGAAGCAGGT-AGAAGCA
66 CTCAAAGTGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCA-AAGCA
* *
7665 ATAAAATGGTTATCTTCCTGATGAGATACTGAGAAGTGAACCAAATTTGCCTTCCTGATGAGATA
130 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATA
*
7730 TAGAGAAGCGGATTG
195 CAGAGAAGCGGATTG
* * *
7745 AAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGAAGGCCAAATCAATGAAACCAAG
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG
* * * * * *
7810 CTCAAAGTAAGCAAATCTTCGAACCCTAACTTCCTGATGAGATGCTGAGAAGCAGGTCGAAGCAA
66 CTCAAAGTGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAA
* * * * * *
7875 T--AA-----AG----C-GATTACATACAGAGAAGTGAACCAGATTTGTCTTCCTGATGAGATAC
131 TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATAC
*
7928 AGAGAAGTGGATTG
196 AGAGAAGCGGATTG
* *
7942 AAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAATAGACCAAA
1 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAA
7993 ACAACGACAC
Statistics
Matches: 606, Mismatches: 57, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
197 100 0.17
198 1 0.00
202 1 0.00
207 2 0.00
208 1 0.00
209 432 0.71
210 69 0.11
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (209 bp):
AAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAG
CTCAAAGTGAGCAAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAA
TAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATAC
AGAGAAGCGGATTG
Done.